Job ID = 14520522 SRX = SRX11781171 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3651884 spots for SRR15481114/SRR15481114.sra Written 3651884 spots for SRR15481114/SRR15481114.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:21 3651884 reads; of these: 3651884 (100.00%) were paired; of these: 2580729 (70.67%) aligned concordantly 0 times 990009 (27.11%) aligned concordantly exactly 1 time 81146 (2.22%) aligned concordantly >1 times ---- 2580729 pairs aligned concordantly 0 times; of these: 23631 (0.92%) aligned discordantly 1 time ---- 2557098 pairs aligned 0 times concordantly or discordantly; of these: 5114196 mates make up the pairs; of these: 3076903 (60.16%) aligned 0 times 1823956 (35.66%) aligned exactly 1 time 213337 (4.17%) aligned >1 times 57.87% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 183909 / 1094382 = 0.1680 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:20:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 19:20:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:20:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:20:44: 1000000 INFO @ Sat, 15 Jan 2022 19:20:49: 2000000 INFO @ Sat, 15 Jan 2022 19:20:55: 3000000 INFO @ Sat, 15 Jan 2022 19:20:59: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:20:59: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:20:59: #1 total tags in treatment: 889458 INFO @ Sat, 15 Jan 2022 19:20:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:20:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:20:59: #1 tags after filtering in treatment: 528685 INFO @ Sat, 15 Jan 2022 19:20:59: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 15 Jan 2022 19:20:59: #1 finished! INFO @ Sat, 15 Jan 2022 19:20:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:20:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:20:59: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 19:20:59: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Jan 2022 19:20:59: start model_add_line... INFO @ Sat, 15 Jan 2022 19:20:59: start X-correlation... INFO @ Sat, 15 Jan 2022 19:20:59: end of X-cor INFO @ Sat, 15 Jan 2022 19:20:59: #2 finished! INFO @ Sat, 15 Jan 2022 19:20:59: #2 predicted fragment length is 254 bps INFO @ Sat, 15 Jan 2022 19:20:59: #2 alternative fragment length(s) may be 1,153,200,230,254,270,583 bps INFO @ Sat, 15 Jan 2022 19:20:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.05_model.r INFO @ Sat, 15 Jan 2022 19:20:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:20:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:21:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:21:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:21:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:21:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.05_summits.bed INFO @ Sat, 15 Jan 2022 19:21:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (13 records, 4 fields): 1 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:21:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 19:21:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:21:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:21:14: 1000000 INFO @ Sat, 15 Jan 2022 19:21:20: 2000000 INFO @ Sat, 15 Jan 2022 19:21:26: 3000000 INFO @ Sat, 15 Jan 2022 19:21:31: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:21:31: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:21:31: #1 total tags in treatment: 889458 INFO @ Sat, 15 Jan 2022 19:21:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:21:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:21:31: #1 tags after filtering in treatment: 528685 INFO @ Sat, 15 Jan 2022 19:21:31: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 15 Jan 2022 19:21:31: #1 finished! INFO @ Sat, 15 Jan 2022 19:21:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:21:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:21:31: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 19:21:31: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Jan 2022 19:21:31: start model_add_line... INFO @ Sat, 15 Jan 2022 19:21:31: start X-correlation... INFO @ Sat, 15 Jan 2022 19:21:31: end of X-cor INFO @ Sat, 15 Jan 2022 19:21:31: #2 finished! INFO @ Sat, 15 Jan 2022 19:21:31: #2 predicted fragment length is 254 bps INFO @ Sat, 15 Jan 2022 19:21:31: #2 alternative fragment length(s) may be 1,153,200,230,254,270,583 bps INFO @ Sat, 15 Jan 2022 19:21:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.10_model.r INFO @ Sat, 15 Jan 2022 19:21:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:21:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:21:33: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:21:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:21:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:21:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.10_summits.bed INFO @ Sat, 15 Jan 2022 19:21:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:21:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 19:21:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:21:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:21:44: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:21:50: 2000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:21:56: 3000000 INFO @ Sat, 15 Jan 2022 19:22:01: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:22:01: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:22:01: #1 total tags in treatment: 889458 INFO @ Sat, 15 Jan 2022 19:22:01: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:22:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:22:01: #1 tags after filtering in treatment: 528685 INFO @ Sat, 15 Jan 2022 19:22:01: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 15 Jan 2022 19:22:01: #1 finished! INFO @ Sat, 15 Jan 2022 19:22:01: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:22:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:22:01: #2 number of paired peaks: 169 WARNING @ Sat, 15 Jan 2022 19:22:01: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sat, 15 Jan 2022 19:22:01: start model_add_line... INFO @ Sat, 15 Jan 2022 19:22:01: start X-correlation... INFO @ Sat, 15 Jan 2022 19:22:01: end of X-cor INFO @ Sat, 15 Jan 2022 19:22:01: #2 finished! INFO @ Sat, 15 Jan 2022 19:22:01: #2 predicted fragment length is 254 bps INFO @ Sat, 15 Jan 2022 19:22:01: #2 alternative fragment length(s) may be 1,153,200,230,254,270,583 bps INFO @ Sat, 15 Jan 2022 19:22:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.20_model.r INFO @ Sat, 15 Jan 2022 19:22:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:22:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:22:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:22:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:22:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:22:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781171/SRX11781171.20_summits.bed INFO @ Sat, 15 Jan 2022 19:22:03: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling